diff env/lib/python3.9/site-packages/networkx/readwrite/pajek.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/networkx/readwrite/pajek.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,284 @@
+"""
+*****
+Pajek
+*****
+Read graphs in Pajek format.
+
+This implementation handles directed and undirected graphs including
+those with self loops and parallel edges.
+
+Format
+------
+See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
+for format information.
+
+"""
+
+import warnings
+
+import networkx as nx
+from networkx.utils import open_file
+
+__all__ = ["read_pajek", "parse_pajek", "generate_pajek", "write_pajek"]
+
+
+def generate_pajek(G):
+    """Generate lines in Pajek graph format.
+
+    Parameters
+    ----------
+    G : graph
+       A Networkx graph
+
+    References
+    ----------
+    See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
+    for format information.
+    """
+    if G.name == "":
+        name = "NetworkX"
+    else:
+        name = G.name
+    # Apparently many Pajek format readers can't process this line
+    # So we'll leave it out for now.
+    # yield '*network %s'%name
+
+    # write nodes with attributes
+    yield f"*vertices {G.order()}"
+    nodes = list(G)
+    # make dictionary mapping nodes to integers
+    nodenumber = dict(zip(nodes, range(1, len(nodes) + 1)))
+    for n in nodes:
+        # copy node attributes and pop mandatory attributes
+        # to avoid duplication.
+        na = G.nodes.get(n, {}).copy()
+        x = na.pop("x", 0.0)
+        y = na.pop("y", 0.0)
+        try:
+            id = int(na.pop("id", nodenumber[n]))
+        except ValueError as e:
+            e.args += (
+                (
+                    "Pajek format requires 'id' to be an int()."
+                    " Refer to the 'Relabeling nodes' section."
+                ),
+            )
+            raise
+        nodenumber[n] = id
+        shape = na.pop("shape", "ellipse")
+        s = " ".join(map(make_qstr, (id, n, x, y, shape)))
+        # only optional attributes are left in na.
+        for k, v in na.items():
+            if isinstance(v, str) and v.strip() != "":
+                s += f" {make_qstr(k)} {make_qstr(v)}"
+            else:
+                warnings.warn(
+                    f"Node attribute {k} is not processed. {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}."
+                )
+        yield s
+
+    # write edges with attributes
+    if G.is_directed():
+        yield "*arcs"
+    else:
+        yield "*edges"
+    for u, v, edgedata in G.edges(data=True):
+        d = edgedata.copy()
+        value = d.pop("weight", 1.0)  # use 1 as default edge value
+        s = " ".join(map(make_qstr, (nodenumber[u], nodenumber[v], value)))
+        for k, v in d.items():
+            if isinstance(v, str) and v.strip() != "":
+                s += f" {make_qstr(k)} {make_qstr(v)}"
+            else:
+                warnings.warn(
+                    f"Edge attribute {k} is not processed. {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}."
+                )
+        yield s
+
+
+@open_file(1, mode="wb")
+def write_pajek(G, path, encoding="UTF-8"):
+    """Write graph in Pajek format to path.
+
+    Parameters
+    ----------
+    G : graph
+       A Networkx graph
+    path : file or string
+       File or filename to write.
+       Filenames ending in .gz or .bz2 will be compressed.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_pajek(G, "test.net")
+
+    Warnings
+    --------
+    Optional node attributes and edge attributes must be non-empty strings.
+    Otherwise it will not be written into the file. You will need to
+    convert those attributes to strings if you want to keep them.
+
+    References
+    ----------
+    See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
+    for format information.
+    """
+    for line in generate_pajek(G):
+        line += "\n"
+        path.write(line.encode(encoding))
+
+
+@open_file(0, mode="rb")
+def read_pajek(path, encoding="UTF-8"):
+    """Read graph in Pajek format from path.
+
+    Parameters
+    ----------
+    path : file or string
+       File or filename to write.
+       Filenames ending in .gz or .bz2 will be uncompressed.
+
+    Returns
+    -------
+    G : NetworkX MultiGraph or MultiDiGraph.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_pajek(G, "test.net")
+    >>> G = nx.read_pajek("test.net")
+
+    To create a Graph instead of a MultiGraph use
+
+    >>> G1 = nx.Graph(G)
+
+    References
+    ----------
+    See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
+    for format information.
+    """
+    lines = (line.decode(encoding) for line in path)
+    return parse_pajek(lines)
+
+
+def parse_pajek(lines):
+    """Parse Pajek format graph from string or iterable.
+
+    Parameters
+    ----------
+    lines : string or iterable
+       Data in Pajek format.
+
+    Returns
+    -------
+    G : NetworkX graph
+
+    See Also
+    --------
+    read_pajek()
+
+    """
+    import shlex
+
+    # multigraph=False
+    if isinstance(lines, str):
+        lines = iter(lines.split("\n"))
+    lines = iter([line.rstrip("\n") for line in lines])
+    G = nx.MultiDiGraph()  # are multiedges allowed in Pajek? assume yes
+    labels = []  # in the order of the file, needed for matrix
+    while lines:
+        try:
+            l = next(lines)
+        except:  # EOF
+            break
+        if l.lower().startswith("*network"):
+            try:
+                label, name = l.split(None, 1)
+            except ValueError:
+                # Line was not of the form:  *network NAME
+                pass
+            else:
+                G.graph["name"] = name
+        elif l.lower().startswith("*vertices"):
+            nodelabels = {}
+            l, nnodes = l.split()
+            for i in range(int(nnodes)):
+                l = next(lines)
+                try:
+                    splitline = [
+                        x.decode("utf-8") for x in shlex.split(str(l).encode("utf-8"))
+                    ]
+                except AttributeError:
+                    splitline = shlex.split(str(l))
+                id, label = splitline[0:2]
+                labels.append(label)
+                G.add_node(label)
+                nodelabels[id] = label
+                G.nodes[label]["id"] = id
+                try:
+                    x, y, shape = splitline[2:5]
+                    G.nodes[label].update(
+                        {"x": float(x), "y": float(y), "shape": shape}
+                    )
+                except:
+                    pass
+                extra_attr = zip(splitline[5::2], splitline[6::2])
+                G.nodes[label].update(extra_attr)
+        elif l.lower().startswith("*edges") or l.lower().startswith("*arcs"):
+            if l.lower().startswith("*edge"):
+                # switch from multidigraph to multigraph
+                G = nx.MultiGraph(G)
+            if l.lower().startswith("*arcs"):
+                # switch to directed with multiple arcs for each existing edge
+                G = G.to_directed()
+            for l in lines:
+                try:
+                    splitline = [
+                        x.decode("utf-8") for x in shlex.split(str(l).encode("utf-8"))
+                    ]
+                except AttributeError:
+                    splitline = shlex.split(str(l))
+
+                if len(splitline) < 2:
+                    continue
+                ui, vi = splitline[0:2]
+                u = nodelabels.get(ui, ui)
+                v = nodelabels.get(vi, vi)
+                # parse the data attached to this edge and put in a dictionary
+                edge_data = {}
+                try:
+                    # there should always be a single value on the edge?
+                    w = splitline[2:3]
+                    edge_data.update({"weight": float(w[0])})
+                except:
+                    pass
+                    # if there isn't, just assign a 1
+                #                    edge_data.update({'value':1})
+                extra_attr = zip(splitline[3::2], splitline[4::2])
+                edge_data.update(extra_attr)
+                # if G.has_edge(u,v):
+                #     multigraph=True
+                G.add_edge(u, v, **edge_data)
+        elif l.lower().startswith("*matrix"):
+            G = nx.DiGraph(G)
+            adj_list = (
+                (labels[row], labels[col], {"weight": int(data)})
+                for (row, line) in enumerate(lines)
+                for (col, data) in enumerate(line.split())
+                if int(data) != 0
+            )
+            G.add_edges_from(adj_list)
+
+    return G
+
+
+def make_qstr(t):
+    """Returns the string representation of t.
+    Add outer double-quotes if the string has a space.
+    """
+    if not isinstance(t, str):
+        t = str(t)
+    if " " in t:
+        t = f'"{t}"'
+    return t